Plot hole: The whole problem with the teleporter occurs when fly DNA is mixed in with Seth Brundle's DNA, starting his transformation into the Brundlefly. Brundle is on a hiding to nothing from the word go, and the fly is irrelevant. Humans are a walking talking mass of foreign DNA - we are host to one trillion bacteria all of which has a complete complement of DNA, as do various tiny mites that live in our hair follicles and all sorts of single cell organisms in our gut. If the transporter serves to mix the DNA of all living creatures which are in the transporter pod at the time Brundle would turn into a half-man, half-bacteria. Incidentally, DNA from a bacteria, an amoeba or a hair follicle mite would be just as 'compatible' with human DNA as that from an insect. It's quite a simple chemical, really.
Plot hole: How did Tommy get Jason's mask? I don't think the police would let him keep it as a souvenir.
Suggested correction: This is not the same mask from the previous movie.
Yes, it is. It even has the ax mark from the end of the third movie.
It is a very different mask. The only things that match are the shape and the axe wound. The color changed from yellow to almond. The straps changed and snap on buttons that attached the straps were replaced with rivets. The half missing large red chevron has been replaced with a red triangle. The two smaller triangles under the eyes are gone. All the damage and chipped paint from part 4 is missing. This mask has more in common with the mask in Tommy's dream in part 5. My opinion - Tommy made it.
Plot hole: Near the end of the movie, when Packard is about to race the Turbo, he puts on a helmet. Where exactly did he keep this helmet? The '77 Corvette is a two-seater with very little storage space for the passengers. Oggie and Minty's helmets could have been in the back seats of their cars.
Plot hole: When the bullies take revenge on Marty, they doctor the chemicals he is preparing so that they explode. The bullies were punished some time in the afternoon, judging by the sun in the very first shot. Their detention is at 4:30 in the afternoon. Somehow, they manage to acquire the necessary chemicals for the explosion within a couple of hours, even though they are stuck at school. In addition to this, they have no way of knowing what chemicals Marty is preparing, so even if they were able to get chemicals, they would not know which ones to get to destroy his experiment.
Suggested correction: Being as how the bacteria and mites and such were IN or ON Seth, the machine was able to organize those symbiotic relationships accordingly as teleporting one would teleport all. The fly was separate, not touching. The machine was not programmed to anticipate two separated entities and so combined them into one on the other side.
Phixius ★
We leave behind a vapour trail of bacteria and viruses (among other things) as we walk, in our breath and emanations from pores in our skin, and Brundle isn't trapping any in his clothes as he isn't wearing any. Brundle has an invisible cloud of DNA floating around him in that teleportation chamber and as far as the machine is concerned their DNA has exactly the same status as that of the fly.
We don't know enough about how the machine works to determine how it might differentiate different DNA types. Unexplained science means it's somehow able to do it. Willing suspension of disbelief for the win.